# Re: extra bonds

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Jul 02 2015 - 09:48:22 CDT

Hi Lara,

I think you would benefit from reading up a bit more on the CHARMM force
field, and what the individual terms mean. The NAMD tutorial has some
more detailed explanations
(http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win-html/node26.html#bondstretch,
http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/node5.html),
but basically you will want to use the first specification, since you
want to keep the sugar at a specific pucker, which can be done with
harmonically constrained dihedral angles going around the ring (ie. the
potential you want to add is like k*(phi-ref)^2). The second
specification is if you want to add another k*(1+cos(n*phi-ref))
potential term. Impropers are "fake" dihedrals that do not describe
rotation about a bond, and are usually used to keep a planar part of the
molecule planar.

The size of k depends on how big of a tolerance you have for deviations
from the ideal geometry. kT at room temperature is ~0.6 kcal/mol. How
much deviation are you willing to tolerate when you run your simulation?

-Josh Vermaas

On 07/02/2015 09:20 AM, Lara rajam wrote:
> Dear NAMD users !
>
> I would like to fix the sugar puckering during the simulation.
> how it should be done in NAMD , do i need to use the dihedral or the
> improper flag in the extra bonds.
>
> I have read through and got information like
>
> * dihedral <atom> <atom> <atom> <atom> <k> <ref>
> * dihedral <atom> <atom> <atom> <atom> <k> <n> <ref>
> * improper <atom> <atom> <atom> <atom> <k> <ref>
> * improper <atom> <atom> <atom> <atom> <k> <n> <ref>
>
> my question is K refers to the spring constant , what should be the
> value given to it and what does the other flag n refer to .
>
> if more information is given it will improve my understanding !
>
> thank you !

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